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ijp-biop-run-macro/results/SingleWindowDisplay.java
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SingleWindowDisplay.java
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package results;
import fiji.util.gui.JImagePanel;
import gadgets.DataContainer;
import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.gui.Line;
import ij.gui.Overlay;
import ij.process.ImageProcessor;
import ij.text.TextWindow;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Panel;
import java.awt.datatransfer.Clipboard;
import java.awt.datatransfer.ClipboardOwner;
import java.awt.datatransfer.StringSelection;
import java.awt.datatransfer.Transferable;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JEditorPane;
import javax.swing.JFrame;
import javax.swing.JScrollPane;
import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.LongType;
import algorithms.AutoThresholdRegression;
import algorithms.Histogram2D;
/**
* This class displays the container contents in one single window
* and offers features like the use of different LUTs.
*
*/
public class SingleWindowDisplay<T extends RealType<T>> extends JFrame implements ResultHandler<T>, ItemListener, ActionListener, ClipboardOwner {
private static final long serialVersionUID = -5642321584354176878L;
protected static final int WIN_WIDTH = 350;
protected static final int WIN_HEIGHT = 600;
// a static list for keeping track of all other SingleWindowDisplays
protected static ArrayList<SingleWindowDisplay<?>> displays = new ArrayList<SingleWindowDisplay<?>>();
// indicates if original images should be displayed or not
protected boolean displayOriginalImages = false;
// this is the image currently selected by the drop down menu
protected RandomAccessibleInterval<? extends RealType<?>> currentlyDisplayedImageResult;
// a list of the available result images, no matter what specific kinds
protected List< NamedContainer< RandomAccessibleInterval<? extends RealType<?>>> > listOfImages
= new ArrayList< NamedContainer< RandomAccessibleInterval<? extends RealType<?>>> >();
protected Map<RandomAccessibleInterval<LongType>, Histogram2D<T>> mapOf2DHistograms
= new HashMap<RandomAccessibleInterval<LongType>, Histogram2D<T>>();
// a list of warnings
protected List<Warning> warnings = new ArrayList<Warning>();
// a list of named values, collected from algorithms
protected List<ValueResult> valueResults = new ArrayList<ValueResult>();
/* a map of images and corresponding LUTs. When an image is not in
* there no LUT should be applied.
*/
protected Map<Object, String> listOfLUTs = new HashMap<Object, String>();
//make a cursor so we can get pixel values from the image
protected RandomAccess<? extends RealType<?>> pixelAccessCursor;
// A PDF writer to call if user wants PDF print
protected PDFWriter<T> pdfWriter;
// The current image
protected ImagePlus imp;
// GUI elements
protected JImagePanel imagePanel;
protected JButton listButton, copyButton;
protected JCheckBox log;
/* The data container with general information about
* source images
*/
protected DataContainer<T> dataContainer = null;
public SingleWindowDisplay(DataContainer<T> container, PDFWriter<T> pdfWriter){
super("Colocalisation " + container.getSourceImage1Name() + " vs " +
container.getSourceImage2Name());
setPreferredSize(new Dimension(WIN_WIDTH, WIN_HEIGHT));
// save a reference to the container
dataContainer = container;
this.pdfWriter = pdfWriter;
// don't show ourself on instantiation
this.setVisible(false);
// add ourself to the list of single window displays
displays.add(this);
}
public void setup() {
JComboBox dropDownList = new JComboBox();
for(NamedContainer< RandomAccessibleInterval<? extends RealType<?>> > img : listOfImages) {
dropDownList.addItem(
new NamedContainer<RandomAccessibleInterval<? extends RealType<?>> >(
img.object, img.name));
}
dropDownList.addItemListener(this);
imagePanel = new JImagePanel(ij.IJ.createImage("dummy", "8-bit", 10, 10, 1));
// Create something to display it in
final JEditorPane editor = new JEditorPane();
editor.setEditable(false); // we're browsing not editing
editor.setContentType("text/html"); // must specify HTML text
editor.setText(makeHtmlText()); // specify the text to display
// Put the JEditorPane in a scrolling window and add it
JScrollPane scrollPane = new JScrollPane(editor);
scrollPane.setPreferredSize(new Dimension(256, 150));
Panel buttons = new Panel();
buttons.setLayout(new FlowLayout(FlowLayout.RIGHT));
// add button for data display of histograms
listButton = new JButton("List");
listButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
showList();
}
});
buttons.add(listButton);
// add button for data copy of histograms
copyButton = new JButton("Copy");
copyButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent arg0) {
copyToClipboard();
}
});
buttons.add(copyButton);
// add button for PDF printing
JButton pdfButten = new JButton("PDF");
pdfButten.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent arg0) {
pdfWriter.process();
}
});
buttons.add(pdfButten);
/* We want the image to be log scale by default
* so the user can see something.
*/
log = new JCheckBox("Log");
log.setSelected(true);
log.addActionListener(this);
buttons.add(log);
final GridBagLayout layout = new GridBagLayout();
final Container pane = getContentPane();
getContentPane().setLayout(layout);
final GridBagConstraints c = new GridBagConstraints();
c.fill = GridBagConstraints.BOTH;
c.weightx = 1;
c.gridwidth = GridBagConstraints.BOTH;
c.gridy++;
pane.add(dropDownList, c);
c.gridy++; c.weighty = 1;
pane.add(imagePanel, c);
c.gridy++; c.weighty = 1;
pane.add(scrollPane, c);
c.weighty = 0; c.gridy++;
pane.add(buttons, c);
pack();
}
public void process() {
// if wanted, display source images
if ( displayOriginalImages ) {
listOfImages.add( new NamedContainer<RandomAccessibleInterval<? extends RealType<?>> >(
dataContainer.getSourceImage1(),
dataContainer.getSourceImage1Name() ) );
listOfImages.add( new NamedContainer<RandomAccessibleInterval<? extends RealType<?>> >(
dataContainer.getSourceImage2(),
dataContainer.getSourceImage2Name() ) );
}
// create HTML table
makeHtmlText();
// set up the GUI
setup();
// display the first image available, if any
if (listOfImages.size() > 0) {
adjustDisplayedImage(listOfImages.get(0).object);
}
// show the GUI
this.setVisible(true);
}
public void handleImage(RandomAccessibleInterval<T> image, String name) {
listOfImages.add( new NamedContainer<RandomAccessibleInterval<? extends RealType<?>> >(
image, name ) );
}
public void handleHistogram(Histogram2D<T> histogram, String name) {
listOfImages.add( new NamedContainer<RandomAccessibleInterval<? extends RealType<?>> >(
histogram.getPlotImage(), name ) );
mapOf2DHistograms.put(histogram.getPlotImage(), histogram);
// link the histogram to a LUT
listOfLUTs.put(histogram.getPlotImage(), "Fire");
}
public void handleWarning(Warning warning) {
warnings.add( warning );
}
public void handleValue(String name, double value) {
handleValue(name, value, 3);
}
public void handleValue(String name, double value, int decimals) {
valueResults.add( new ValueResult(name, value, decimals));
}
/**
* Prints an HTML table entry onto the stream.
*/
protected void printTableRow(PrintWriter out, String name, String text) {
out.print("<TR><TD>" + name + "</TD><TD>" + text + "</TD></TR");
}
/**
* Prints an HTML table entry onto the stream.
*/
protected void printTableRow(PrintWriter out, String name, double number) {
printTableRow(out, name, number, 3);
}
/**
* Prints an HTML table entry onto the stream.
*/
protected void printTableRow(PrintWriter out, String name, double number, int decimalPlaces) {
printTableRow(out, name, IJ.d2s(number, decimalPlaces));
}
/**
* This method creates CSS formatted HTML source out of the
* results stored in the member variables and adds some
* image statistics found in the data container.
* @return The HTML source to display
*/
protected String makeHtmlText() {
StringWriter sout = new StringWriter();
PrintWriter out = new PrintWriter( sout );
out.print("<html><head>");
// add some style information
out.print("<style type=\"text/css\">"
+ "body {font-size: 9px; font-family: sans-serif;}"
+ "h1 {color: black; font-weight: bold; font-size: 10px;}"
+ "h1.warn {color: red;}"
+ "h1.nowarn {color: green;}"
+ "table {width: auto;}"
+ "td { border-width:1px; border-style: solid; vertical-align:top; overflow:hidden;}"
+ "</style>");
out.print("</head>");
// print out warnings, if any
if ( warnings.size() > 0 ) {
out.print("<H1 class=\"warn\">Warnings</H1>");
// Print out the table
out.print("<TABLE class=\"warn\"><TR>");
out.print("<TH>Type</TH><TH>Message</TH></TR>");
for (Warning w : warnings) {
printTableRow(out, w.getShortMessage(), w.getLongMessage());
}
out.println("</TABLE>");
} else {
out.print("<H1 class=\"nowarn\">No warnings occured</H1>");
}
// print out simple value results
out.print("<H1>Results</H1>");
// Print out the table
out.print("<TABLE><TR>");
out.print("<TH>Name</TH><TH>Result</TH></TR>");
for ( ValueResult vr : valueResults) {
printTableRow(out, vr.name, vr.number, vr.decimals);
}
out.println("</TABLE>");
// print some image statistics
out.print("<H1>Image statistics</H1>");
out.print("<TABLE>");
printTableRow(out, "Min channel 1", dataContainer.getMinCh1());
printTableRow(out, "Max channel 1", dataContainer.getMaxCh1());
printTableRow(out, "Mean channel 1", dataContainer.getMeanCh1());
printTableRow(out, "Min channel 2", dataContainer.getMinCh2());
printTableRow(out, "Max channel 2", dataContainer.getMaxCh2());
printTableRow(out, "Mean channel 2", dataContainer.getMeanCh2());
out.println("</TABLE>");
out.print("</html>");
out.close();
// Get the string of HTML from the StringWriter and return it.
return sout.toString();
}
/**
* If the currently selected ImageResult is an HistrogramResult,
* a table of x-values, y-values and the counts.
*/
protected void showList() {
/* check if we are dealing with an histogram result
* or a generic image result
*/
if (isHistogram(currentlyDisplayedImageResult)) {
Histogram2D<T> hr = mapOf2DHistograms.get(currentlyDisplayedImageResult);
double xBinWidth = 1.0 / hr.getXBinWidth();
double yBinWidth = 1.0 / hr.getYBinWidth();
// check if we have bins of size one or other ones
boolean xBinWidthIsOne = Math.abs(xBinWidth - 1.0) < 0.00001;
boolean yBinWidthIsOne = Math.abs(yBinWidth - 1.0) < 0.00001;
// configure table headings accordingly
String vHeadingX = xBinWidthIsOne ? "X value" : "X bin start";
String vHeadingY = yBinWidthIsOne ? "Y value" : "Y bin start";
// get the actual histogram data
String histogramData = hr.getData();
TextWindow tw = new TextWindow(getTitle(), vHeadingX + "\t" +
vHeadingY + "\tcount", histogramData, 250, 400);
tw.setVisible(true);
}
}
/**
* If the currently selected ImageResult is an HistogramRestult,
* this method copies its data into to the clipboard.
*/
protected void copyToClipboard() {
/* check if we are dealing with an histogram result
* or a generic image result
*/
if (isHistogram(currentlyDisplayedImageResult)) {
/* try to get the system clipboard and return
* if we can't get it
*/
Clipboard systemClipboard = null;
try {
systemClipboard = getToolkit().getSystemClipboard();
} catch (Exception e) {
systemClipboard = null;
}
if (systemClipboard==null) {
IJ.error("Unable to copy to Clipboard.");
return;
}
// copy histogram values
IJ.showStatus("Copying histogram values...");
String text = mapOf2DHistograms.get(currentlyDisplayedImageResult).getData();
StringSelection contents = new StringSelection( text );
systemClipboard.setContents(contents, this);
IJ.showStatus(text.length() + " characters copied to Clipboard");
}
}
public void mouseMoved( final int x, final int y) {
final ImageJ ij = IJ.getInstance();
if (ij != null && currentlyDisplayedImageResult != null) {
/* If Alt key is not pressed, display the calibrated data.
* If not, display image positions and data.
* Non log image intensity from original image or 2D histogram result is always shown in status bar,
* not the log intensity that might actually be displayed in the image.
*/
if (!IJ.altKeyDown()){
// the alt key is not pressed use x and y values that are bin widths or calibrated intensities not the x y image coordinates.
if (isHistogram(currentlyDisplayedImageResult)) {
Histogram2D<T> histogram = mapOf2DHistograms.get(currentlyDisplayedImageResult);
synchronized( pixelAccessCursor )
{
// set position of output cursor
pixelAccessCursor.setPosition(x, 0);
pixelAccessCursor.setPosition(y, 1);
// get current value at position
RandomAccess<LongType> cursor = (RandomAccess<LongType>)pixelAccessCursor;
long val = cursor.get().getIntegerLong();
double calibratedXBinBottom = histogram.getXMin() + x / histogram.getXBinWidth();
double calibratedXBinTop = histogram.getXMin() + (x + 1) / histogram.getXBinWidth();
double calibratedYBinBottom = histogram.getYMin() + y / histogram.getYBinWidth();
double calibratedYBinTop = histogram.getYMin() + (y + 1) / histogram.getYBinWidth();
IJ.showStatus("x = " + IJ.d2s(calibratedXBinBottom) + " to " + IJ.d2s(calibratedXBinTop) +
", y = " + IJ.d2s(calibratedYBinBottom) + " to " + IJ.d2s(calibratedYBinTop) + ", value = " + val );
}
} else {
RandomAccessibleInterval<T> img = (RandomAccessibleInterval<T>) currentlyDisplayedImageResult;
ImagePlus imp = ImageJFunctions.wrapFloat( img, "TODO" );
imp.mouseMoved(x, y);
}
} else {
// alt key is down, so show the image coordinates for x y in status bar.
RandomAccessibleInterval<T> img = (RandomAccessibleInterval<T>) currentlyDisplayedImageResult;
ImagePlus imp = ImageJFunctions.wrapFloat( img, "TODO" );
imp.mouseMoved(x, y);
}
}
}
/**
* Draws the passed ImageResult on the ImagePlus of this class.
* If the image is part of a CompositeImageResult then contained
* lines will also be drawn
*/
protected void drawImage(RandomAccessibleInterval<? extends RealType<?>> img) {
// get ImgLib image as ImageJ image
imp = ImageJFunctions.wrapFloat( (RandomAccessibleInterval<T>) img, "TODO" );
imagePanel.updateImage(imp);
// set the display range
// check if a LUT should be applied
if ( listOfLUTs.containsKey(img) ) {
// select linked look up table
IJ.run(imp, listOfLUTs.get(img), null);
}
imp.getProcessor().resetMinAndMax();
boolean overlayModified = false;
Overlay overlay = new Overlay();
// if it is the 2d histogram, we want to show the regression line
if (isHistogram(img)) {
Histogram2D<T> histogram = mapOf2DHistograms.get(img);
/* check if we should draw a regression line for the
* current histogram.
*/
if ( histogram.getDrawingSettings().contains(Histogram2D.DrawingFlags.RegressionLine) ) {
AutoThresholdRegression<T> autoThreshold = dataContainer.getAutoThreshold();
if (histogram != null && autoThreshold != null) {
if (img == histogram.getPlotImage()) {
drawLine(overlay, img,
autoThreshold.getAutoThresholdSlope(),
autoThreshold.getAutoThresholdIntercept());
overlayModified = true;
}
}
}
}
if (overlayModified) {
overlay.setStrokeColor(java.awt.Color.WHITE);
imp.setOverlay(overlay);
}
imagePanel.repaint();
}
/**
* Tests whether the given image is a histogram or not.
* @param img The image to test
* @return true if histogram, false otherwise
*/
protected boolean isHistogram(RandomAccessibleInterval<? extends RealType<?>> img) {
return mapOf2DHistograms.containsKey(img);
}
/**
* Draws the line on the overlay.
*/
protected void drawLine(Overlay overlay, RandomAccessibleInterval<? extends RealType<?>> img,
double slope, double intercept) {
double startX, startY, endX, endY;
long imgWidth = img.dimension(0);
long imgHeight = img.dimension(1);
/* since we want to draw the line over the whole image
* we can directly use screen coordinates for x values.
*/
startX = 0.0;
endX = imgWidth;
// check if we can get some exta information for drawing
if (isHistogram(img)) {
Histogram2D<T> histogram = mapOf2DHistograms.get(img);
// get calibrated start y coordinates
double calibratedStartY = slope * histogram.getXMin() + intercept;
double calibratedEndY = slope * histogram.getXMax() + intercept;
// convert calibrated coordinates to screen coordinates
startY = calibratedStartY * histogram.getYBinWidth();
endY = calibratedEndY * histogram.getYBinWidth();
} else {
startY = slope * startX + intercept;
endY = slope * endX + intercept;
}
/* since the screen origin is in the top left
* of the image, we need to x-mirror our line
*/
startY = ( imgHeight - 1 ) - startY;
endY = ( imgHeight - 1 ) - endY;
// create the line ROI and add it to the overlay
Line lineROI = new Line(startX, startY, endX, endY);
/* Set drawing width of line to one, in case it has
* been changed globally.
*/
lineROI.setStrokeWidth(1.0f);
overlay.add(lineROI);
}
protected void adjustDisplayedImage (RandomAccessibleInterval<? extends RealType<?>> img) {
/* when changing the result image to display
* need to set the image we were looking at
* back to not log scale,
* so we don't log it twice if its reselected.
*/
if (log.isSelected())
toggleLogarithmic(false);
currentlyDisplayedImageResult = img;
pixelAccessCursor = img.randomAccess();
// Currently disabled, due to lag of non-histograms :-)
// disable list and copy button if it is no histogram result
listButton.setEnabled( isHistogram(img) );
copyButton.setEnabled( isHistogram(img) );
drawImage(img);
toggleLogarithmic(log.isSelected());
// ensure a valid layout, we changed the image
getContentPane().validate();
getContentPane().repaint();
}
public void itemStateChanged(ItemEvent e) {
if (e.getStateChange() == ItemEvent.SELECTED) {
RandomAccessibleInterval<? extends RealType<?>> img =
((NamedContainer<RandomAccessibleInterval<? extends RealType<?>> >)(e.getItem())).getObject();
adjustDisplayedImage(img);
}
}
protected void toggleLogarithmic(boolean enabled){
if (imp == null)
return;
ImageProcessor ip = imp.getProcessor();
if (enabled) {
ip.snapshot();
ip.log();
ip.resetMinAndMax();
}
else
ip.reset();
imagePanel.repaint();
}
public void actionPerformed(ActionEvent e) {
if (e.getSource() == log) {
toggleLogarithmic(log.isSelected());
}
}
public void lostOwnership(Clipboard clipboard, Transferable contents) {
// nothing to do here
}
}
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